Brain data

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
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Load data plot it

dataset.load()
dataset.data_type
'brain'
fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'

fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'

fig_wm.display('jupyter-book', tissue = 'WM')

Spine

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

dataset.load()
dataset.data['T1w']
--2022-06-02 02:08:35--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20210610/spinalcord_results.zip
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Subject Session Timestamp SCT Version Filename Slice (I->S) VertLevel MEAN(area) STD(area) MEAN(angle_AP) ... STD(diameter_AP) MEAN(diameter_RL) STD(diameter_RL) MEAN(eccentricity) STD(eccentricity) MEAN(orientation) STD(orientation) MEAN(solidity) STD(solidity) SUM(length)
1 1 1 2021-06-09 23:24:10 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 31:75 2:3 67.680431 1.598728 -4.254822 ... 0.225578 10.843164 0.307774 0.680936 0.039585 2.149545 1.734302 0.980308 0.009615 36.167347
6 1 2 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 47:86 2:3 67.511930 1.726861 -6.577358 ... 0.186145 10.874612 0.275935 0.690540 0.031751 2.855729 1.967201 0.977647 0.008612 32.528253
0 1 3 2021-06-09 23:24:08 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:93 2:3 64.109061 3.127582 -4.670983 ... 0.464761 10.640776 0.333651 0.690605 0.054994 3.202127 2.184708 0.976971 0.007494 34.565242
8 2 1 2021-06-09 23:41:15 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 1:38 2:3 66.455289 4.204379 0.095829 ... 0.684070 11.992443 0.585042 0.794791 0.061804 2.234122 1.464966 0.963074 0.016533 31.424022
10 2 2 2021-06-09 23:41:24 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 12:50 2:3 73.688109 2.833139 -0.068322 ... 0.406465 12.065046 0.492764 0.756302 0.053939 2.367144 1.803792 0.966030 0.009791 32.356730
15 2 3 2021-06-09 23:50:43 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 3:39 2:3 73.905494 2.073274 -0.691532 ... 0.368828 12.371408 0.639116 0.780126 0.052688 1.694898 1.187327 0.963111 0.014391 30.534960
12 2 4 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 9:46 2:3 69.405673 4.568637 -0.749008 ... 0.543059 12.227376 0.665839 0.796428 0.053488 2.145301 1.623586 0.958420 0.020529 31.442066
9 3 1 2021-06-09 23:41:20 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:85 2:3 59.927681 1.980624 -0.778617 ... 0.334499 10.086060 0.232852 0.658816 0.049798 2.475063 1.644264 0.972640 0.009458 28.297791
13 3 2 2021-06-09 23:41:42 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 33:66 2:3 60.228814 1.776652 -1.464265 ... 0.247391 10.486967 0.214164 0.716856 0.033921 1.850661 1.538691 0.966100 0.007298 27.236579
11 3 3 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 60.621684 1.733616 -0.009478 ... 0.358365 10.632869 0.308162 0.726909 0.049649 1.681134 1.217510 0.970807 0.010769 28.389363
16 3 4 2021-06-09 23:55:17 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 40:74 2:3 59.915665 2.030933 -2.222570 ... 0.296578 10.445562 0.243935 0.716104 0.038919 2.551453 2.010580 0.972863 0.010084 28.329492
17 4 2 2021-06-09 23:55:38 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 49:84 2:3 59.717857 2.220913 2.572138 ... 0.399145 10.999128 0.354854 0.775108 0.045832 2.195005 1.555832 0.972639 0.015228 29.056988
18 4 3 2021-06-09 23:55:53 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 61.969221 2.026699 6.989458 ... 0.326731 10.956739 0.419218 0.753243 0.040568 2.095929 1.251544 0.976777 0.009427 28.313078
4 5 1 2021-06-09 23:24:18 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 19:57 2:3 53.010013 11.097434 -1.790824 ... 1.087683 10.965275 0.675722 0.822167 0.059414 4.036279 2.295310 0.952220 0.027352 33.355815
14 5 2 2021-06-09 23:41:45 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 44:82 2:3 64.717972 4.153035 -3.034680 ... 0.567947 11.448594 0.408139 0.769825 0.056204 4.103625 1.847953 0.966696 0.012619 32.529064
2 6 1 2021-06-09 23:24:11 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 45:81 2:3 62.953114 1.769023 -0.646246 ... 0.216321 11.513113 0.470660 0.792890 0.029588 1.260913 1.049494 0.965233 0.014776 30.644730
7 6 2 2021-06-09 23:24:21 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 89:125 2:3 64.823566 18.835219 13.113466 ... 1.159209 9.503113 2.506067 0.576338 0.152557 22.042768 32.322329 0.968538 0.032237 10.122137
5 6 3 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 38:75 2:3 62.990802 2.049191 -2.338349 ... 0.298265 11.506661 0.596266 0.792194 0.041279 1.614134 1.158783 0.973527 0.010495 31.364216
3 6 4 2021-06-09 23:24:12 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 58:95 2:3 63.925810 2.765595 -1.132526 ... 0.248317 11.727604 0.490648 0.803257 0.028672 1.754369 1.049329 0.971605 0.012450 31.247426

19 rows × 24 columns

fig_spine = Plot(dataset, plot_name = 'new-fig-2')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'

fig_spine.display('jupyter-book', tissue = 'WM')